Collision-induced conformational changes in glycine

We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes (III-->I and IV-->I), we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters, conformer III has been consistently observed, but conformer IV has yet to be conclusively detected. Because of the calculated thermodynamic stability of conformer IV, its elusiveness has been attributed to the IV-->I conformer interconversion process. However, our calculations present little indication that IV-->I interconversion occurs more readily than III-->I interconversion. Although we cannot determine whether conformer IV interconverts during experimental Ne- and Ar-matrix depositions, our evidence suggests that the conformer should be present in helium droplets. Anharmonic vibrational frequency calculations illustrate that previous efforts to detect conformer IV may have been hindered by the overlap of its IR-absorption bands with those of other conformers. We propose that the redshifted symmetric –CH2 stretch of conformer IV provides a means for its conclusive experimental detection

Tuning the excited state of photoactive building blocks for metal-templated self-assembly.

The reaction of 2,2':4,4'':4',4'''-quaterpyridyl (qtpy), with d(6) ruthenium(II) (Ru(II) ), and rhenium(I) (Re(I) ) metal centers has been investigated. The pendant pyridyl groups on the products have also been methylated to produce a second series of complexes containing coordinated Meqtpy(2+). The absorption spectra of the complexes are dominated by intraligand and charge-transfer bands. The ruthenium(II) complexes display broad unstructured luminescence consistent with emission from a Ru(d)→diimine(π*) manifold in acetonitrile solutions. In aqueous solutions, their emissions are weaker and the lifetimes are shorter. This effect is particularly acute for complexes incorporating coordinated dipyridylpyrazine, dppz, ligands. Although the emission of the ruthenium(II) complexes containing Meqtpy(2+) is generally shorter than their qtpy analogs, it is notable that solvent-dependent effects are much less intense. The rhenium(I) complexes also display broad unstructured luminescence but, compared with the ruthenium(II) systems, they have a relatively short lifetime in acetonitrile. Electrochemical studies reveal that all of the Ru(II) complexes display chemically reversible metal-based oxidations. Re(I) complexes only display irreversible metal-based oxidations. In most cases, the reduction processes were not fully chemically reversible. The electrochemical and optical studies reveal that the nature of the lowest excited state of these complexes--particularly, the systems incorporating dppz--is highly dependent on the nature of the coordinated ligands. Calculations indicate that, although the excited state of most of the complexes is centered on the qtpy or Meqtpy(2+) ligands, the excited state of the complexes containing dppz ligands is switched away from the dppz by qtpy methylation. A crystallographic study on one of the dicationic ruthenium(II) structures reveals that it forms an inclusion complex with benzene

In situ root identification through blade penetrometer testing – Part 2:field testing

The spatial distribution, depths and diameters of roots in soil are difficult to quantify but important to know when reinforcement of a rooted slope or the stability of a plant is to be assessed. Previous work has shown that roots can be detected from the depth–resistance trace measured using a penetrometer with an adapted blade-shaped tip. Theoretical models exist to predict both forces and root displacements associated with root failure in either bending or tension. However, these studies were performed in dry sand under laboratory conditions, using acrylonitrile butadiene styrene root analogues rather than real roots. In this paper blade penetrometer field testing on two forested field sites, with Sitka spruce and pedunculate oak in sandy silt and clayey silt, respectively, is used to evaluate models under field conditions. Root breakages could be detected from blade penetrometer depth–resistance traces and using complementary acoustic measurements. Predictions of additional penetrometer resistance at root failure were more accurate than the displacement predictions. An analytical cable model, assuming roots are flexible and fail in tension, provided the best predictions for Sitka roots, whereas thick oak roots were better predicted assuming bending failure. These matched the modes of failure observed in three-point bending tests of the root material in each case. The presence of significant amounts of gravel made it sometimes difficult to distinguish between hitting a root or a stone. The root diameter could be predicted when root strength and stiffness, and soil penetrometer resistance were known and the right interpretative model was selected. Estimates based on peak force were more accurate than those based on root displacement. This measurement procedure is therefore a potentially valuable tool to quantify the spatial distribution of roots and their reinforcement potential in the field. </jats:p

In situ root identification through blade penetrometer testing – Part 1:interpretative models and laboratory testing

Root architecture and reinforcement are important parameters to measure the safety of vegetated slopes and stream banks against slope instability and erosion or to assess the stability of plants against environmental loading (e.g. windthrow of trees). However, these are difficult to measure without time-consuming sampling or counting procedures. Previous studies proposed using a penetrometer with an adapted geometry, and showed that individual root breakages could be detected as sudden drops in penetrometer resistance. However, there are no existing models to derive root properties from the measured traces. Here, several interpretative models are developed and their performance at identifying and characterising buried acrylonitrile butadiene styrene root analogues of varying diameter and architecture in sand are assessed. It was found that models, assuming the analogues broke in bending rather than tension, provided good predictions for the force–displacement behaviour. The simple analytical bending model developed here was shown to perform almost as well as more sophisticated numerical models. For all models, the predictions of additional penetrometer force required to break the root analogue were more accurate than predictions for lateral root displacement required to reach failure. The root analogue diameter and to a lesser extent the soil resistance and root angle were shown to affect the penetrometer resistance strongly. Root branching, root length and the distance between the point of load application and a root boundary (root tip or parent root) had a much smaller effect. When the root failure mechanism, root strength, root stiffness and soil resistance are known, an accurate prediction of the root diameter can be made based on the root peak resistance value identified from a blade penetration test. Penetrometer testing, a test which is easy to perform in the field, coupled with an accurate interpretative model might therefore be an effective method to rapidly quantify the spatial distribution, depths and diameters of roots. </jats:p

(13)C or Not (13)C: Selective Synthesis of Asymmetric Carbon-13-Labeled Platinum(II) cis-Acetylides.

Asymmetric isotopic labeling of parallel and identical electron- or energy-transfer pathways in symmetrical molecular assemblies is an extremely challenging task owing to the inherent lack of isotopic selectivity in conventional synthetic methods. Yet, it would be a highly valuable tool in the study and control of complex light-matter interactions in molecular systems by exclusively and nonintrusively labeling one of otherwise identical reaction pathways, potentially directing charge and energy transport along a chosen path. Here we describe the first selective synthetic route to asymmetrically labeled organometallic compounds, on the example of charge-transfer platinum(II) cis-acetylide complexes. We demonstrate the selective (13)C labeling of one of two acetylide groups. We further show that such isotopic labeling successfully decouples the two ν(C≡C) in the mid-IR region, permitting independent spectroscopic monitoring of two otherwise identical electron-transfer pathways, along the (12)C≡(12)C and (13)C≡(13)C coordinates. Quantum-mechanical mixing leads to intriguing complex features in the vibrational spectra of such species, which we successfully model by full-dimensional anharmonically corrected DFT calculations, despite the large size of these systems. The synthetic route developed and demonstrated herein should lead to a great diversity of asymmetric organometallic complexes inaccessible otherwise, opening up a plethora of opportunities to advance the fundamental understanding and control of light-matter interactions in molecular systems

Dynamics in the ordered and disordered phases of barocaloric adamantane

High-entropy order-disorder phase transitions can be used for efficient and eco-friendly barocaloric solid-state cooling. Here the barocaloric effect is reported in an archetypal plastic crystal, adamantane. Adamantane has a colossal isothermally reversible entropy change of 106 J K-1 kg-1 . Extremely low hysteresis means that this can be accessed at pressure differences less than 200 bar. Configurational entropy can only account for about 40% of the total entropy change; the remainder is due to vibrational effects. Using neutron spectroscopy and supercell lattice dynamics calculations, it is found that this vibrational entropy change is mainly caused by softening in the high-entropy phase of acoustic modes that correspond to molecular rotations. We attribute this behaviour to the contrast between an 'interlocked' state in the low-entropy phase and sphere-like behaviour in the high-entropy phase. Although adamantane is a simple van der Waals solid with near-spherical molecules, this approach can be leveraged for the design of more complex barocaloric molecular crystals. Moreover, this study shows that supercell lattice dynamics calculations can accurately map the effect of orientational disorder on the phonon spectrum, paving the way for studying the vibrational entropy, thermal conductivity, and other thermodynamic effects in more complex materials.Comment: 14 pages, 6 figure

State-to-state reaction probabilities for the H+O(2)(v,j) -> O+OH(v',j') reaction on three potential energy surfaces

We report state-to-state and total reaction probabilities for J=0 and total reaction probabilities for J=2 and 4 for the title reaction, both for ground-state and initially rovibrationally excited reactants. The results for three different potential energy surfaces are compared and contrasted. The potential energy surfaces employed are the DMBE IV surface by Pastrana [J. Phys. Chem. 94, 8073 (1990)], the surface by Troe and Ushakov (TU) [J. Chem. Phys. 115, 3621 (2001)], and the new XXZLG ab initio surface by Xu [J. Chem. Phys. 122, 244305 (2005)]. Our results show that the total reaction probabilities from both the TU and XXZLG surfaces are much smaller in magnitude for collision energies above 1.2 eV compared to the DMBE IV surface. The three surfaces also show different behavior with regards to the effect of initial state excitation. The reactivity is increased on the XXZLG and the TU surfaces and decreased on the DMBE IV surface. Vibrational and rotational product state distributions for the XXZLG and the DMBE IV surface show different behaviors for both types of distributions. Our results show that for energies above 1.25 eV the dynamics on the DMBE IV surface are not statistical. However, there is also evidence that the dynamics on the XXZLG surface are not purely statistical for energies above the onset of the first excited product vibrational state v'=1. The magnitude of the total reaction probability is decreased for J>0 for the DMBE IV and the XXZLG surfaces for ground-state reactants. However, for initially rovibrationally excited reactants, the total reaction probability does not decrease as expected for both surfaces. As a result the total cross section averaged over all Boltzmann accessible rotational states may well be larger than the cross section reported in the literature for j=1. (C) 2007 American Institute of Physics

Manganese tricarbonyl complexes with asymmetric 2 2‑iminopyridine ligands: toward decoupling steric and electronic 3 factors in electrocatalytic CO2 reduction

Manganese tricarbonyl bromide complexes incorporating IP (2-(phenylimino)pyridine) derivatives, [MnBr(CO)3(IP)], are demonstrated as a new group of catalysts for CO2 reduction, which represent the first example of utilization of (phenylimino)pyridine ligands on manganese centers for this purpose. The key feature is the asymmetric structure of the redox-noninnocent ligand that permits independent tuning of its steric and electronic properties. The α-diimine ligands and five new Mn(I) compounds have been synthesized, isolated in high yields, and fully characterized, including X-ray crystallography. Their electrochemical and electrocatalytic behavior was investigated using cyclic voltammetry and UV−vis−IR spectroelectrochemistry within an OTTLE cell. Mechanistic investigations under an inert atmosphere have revealed differences in the nature of the reduction products as a function of steric bulk of the ligand. The direct ECE (electrochemical−chemical−electrochemical) formation of a five-coordinate anion [Mn(CO)3(IP)]−, a product of two-electron reduction of the parent complex, is observed in the case of the bulky DIPIMP (2-[((2,6-diisopropylphenyl)imino)methyl]pyridine), TBIMP (2-[((2-tert-butylphenyl)imino)methyl]-pyridine), and TBIEP (2-[((2-tert-butylphenyl)imino)ethyl]pyridine) derivatives. This process is replaced for the least sterically demanding IP ligand in [MnBr(CO)3(IMP)] (2-[(phenylimino)methyl]pyridine) by the stepwise formation of such a monoanion via an ECEC(E) mechanism involving also the intermediate Mn−Mn dimer [Mn(CO)3(IMP)]2. The complex [MnBr(CO)3(IPIMP)] (2-[((2-diisopropylphenyl)imino)methyl]pyridine), which carries a moderately electron donating, moderately bulky IP ligand, shows an intermediate behavior where both the five-coordinate anion and its dimeric precursor are jointly detected on the time scale of the spectroelectrochemical experiments. Under an atmosphere of CO2 the studied complexes, except for the DIPIMP derivative, rapidly coordinate CO2, forming stable bicarbonate intermediates, with no dimer being observed. Such behavior indicates that the CO2 binding is outcompeting another pathway: viz., the dimerization reaction between the five-coordinate anion and the neutral parent complex. The bicarbonate intermediate species undergo reduction at more negative potentials (ca. −2.2 V vs Fc/Fc+ ), recovering [Mn(CO)3(IP)]− and triggering the catalytic production of CO

A dinuclear ruthenium(II) phototherapeutic that targets duplex and quadruplex DNA

With the aim of developing a sensitizer for photodynamic therapy, a previously reported luminescent dinuclear complex that functions as a DNA probe in live cells was modified to produce a new isostructural derivative containing RuII(TAP)2 fragments (TAP = 1,4,5,8- tetraazaphenanthrene). The structure of the new complex has been confirmed by a variety of techniques including single crystal X-ray analysis. Unlike its parent, the new complex displays RuL-based 3MLCT emission in both MeCN and water. Results from electrochemical studies and emission quenching experiments involving guanosine monophosphate are consistent with an excited state located on a TAP moiety. This hypothesis is further supported by detailed DFT calculations, which take into account solvent effects on excited state dynamics. Cell-free steady-state and time-resolved optical studies on the interaction of the new complex with duplex and quadruplex DNA show that the complex binds with high affinity to both structures and indicate that its photoexcited state is also quenched by DNA, a process that is accompanied by the generation of the guanine radical cation sites as photo-oxidization products. Like the parent complex, this new compound is taken up by live cells where it primarily localizes within the nucleus and displays low cytotoxicity in the absence of light. However, in complete contrast to [{RuII(phen)2}2(tpphz)]4+, the new complex is therapeutically activated by light to become highly phototoxic toward malignant human melanoma cell line showing that it is a promising lead for the treatment of this recalcitrant cancer.EPSRC grant EP/M015572/1 Unviersity of Sheffield/EPSRC Doctoral Fellowship Prize EPSRC Capital Equipment Award ERASMUS